Amelia Pond's Melody of Silence
by TheEleventhTARDIS
Summary: When a young Amelia Pond is abducted by a secret organization called The Silence for experimentation, she becomes best friends with her quirky and unstable cellmate, a mysterious girl called Mels who has been in their clutches all her life. With a deranged Chemist's blind daughter Ada as their only friend and ally, the girls have 2 options. escape, or enslavement and death.
1. The Harsh Melody

Amelia Pond jolted awake with a scream.

"Mommy!" she cried, tears rolling down her cheeks. "Mom, Rory, help! They're going to get me! Don't let them get me!"

"Its too late kid," said a voice to her right. "they already got you, and no one, especially not your _Mommy_ , is going to rescue you."

Amelia opened her eyes and looked over to the voice with tears in her eyes. She was in a small white room with a set of metal bars that cut straight down the middle. On the other side of the bars, a girl who looked to be about eleven or twelve with frizzy black hair, starched white clothes and a knowing smirk was leaning over and regarding her with a look of boredom mingled with curiosity.

"W-what do you mean?" Amelia whispered. "Where am I?"

"Isn't it obvious?" The girl sighed dramatically. "You're in the Specimen holding block of the Science division of the Silence division of the Alliance headquarters."

"What?!" Amelia asked, more confused by the strange girls flippant tone and quick manner of speaking than the unfamiliar words she used.

"Not the sharpest tool in the shed, are you?" The girl rolled her eyes. "What's the last thing you remember?"

"I-I was playing with Rory in the front yard, and he hurt his knee, so my Mom took him inside to get a band-aid, and then, a-and then-" her voice shook as she remembered the next part. "I was all alone in the front yard, and these really scary looking men came up in a van and grabbed me and put something in my arm and I fell asleep!"

"Yeah, they tranqed you." The girl informed her matter-of-factly. "Don't worry, they do it to everyone they bring in. There shouldn't be any major side effects, but I wouldn't try standing up for a while."

"But, why? Why did they take me? Why am I here?" Amelia sniffled, trying to hold back more tears as the girl sneered at her teary questions.

She missed her parents, and she missed Rory, and she just wanted to go _home!_ Away from the tiny cell, scary men, and unsettling girl who was now staring at her with a look of pity and condescension.

"Cause they need a new guinea pig for Dr. Gillyflower's experiments, duh!" She said with a yawn. "My names Melody by the way, but you can call me Mels." She scowled as Amelia failed to respond, clearly shell-shocked from her tactless explanation. "Well, don't be _rude_ , you crybaby. tell me what your name is!" She demanded haughtily.

"...Amelia Pond." Amelia responded quietly, cheeks burning from Mels' insult. "And I don't want to be here! I want to go home!" She gave up on her losing battle of maintaining her composure and started to cry again.

"Oh quit yer whining, Amy, - _can I call you Amy? I'm gonna call you Amy, Amelia is too much of a mouthful_ \- At least you _had_ a real life, and a family. Probably in Scotland, right? You sound Scottish. Certainly not from around here anyway..." Mels trailed off thoughtfully as she lost her train of thought and looked at the newly renamed 'Amy' expectantly.

"..Oh, um, we used to live in Scotland, but we moved to England last year for my dads work. I didn't like moving very much, but now I really don't like it!" Amy said with a shiver as she looked around the unnaturally white space.

Mels nodded. "Yeah, I thought so..." Suddenly her eyes flashed and she shook herself as if to clear her head. "Anyway, the point _**is** ,_ _'boo hoo,'_ poor little Amelia Pond from _Scotland._ " she spat venomously, her mood changing from curious to livid in a heartbeat. "Compared to me, your life is a god damn Fairytale!" she ignored Amy's scandalized gasp at her cussing and continued to rant, her voice shaking with anger. "I was _born_ in this hell-hole. I've been raised to be a living _weapon_ , and I don't even know what my own _mother_ looks like. you have no reason to be upset about _anything_!"

Amy gaped at her cell mate in shock. Unable to process the overwhelming amount of information Mels had just spewed at her, she blurted out the first question that came to her mind. "How can you not know who your mother is?"

"They tried to tell me that my mother didn't want me and I was 'abandoned as an infant'," Mels scowled as she made air-quotes with her scarred hands. "but I know they're lying."

"How?"

"Cause they lie about everything! They just want me to think I'm unwanted and unloved so they can manipulate me into thinking they're the 'good guys' or something equally stupid. Besides, Ada told me the truth years ago."

"Ada?"

"Yeah, Ada. You'll meet her soon, its almost lunchtime. I'm sure you'll love her. Ada's the only person in this place who's outside of a freaking cage and actually has a soul. She's pretty much the only good thing in my life. Well, besides you."

"Me?!" Amy said in surprise. A moment ago Mels had seemed to hate her!

"Yeah, you." Mels regarded the younger girl thoughtfully. her earlier outburst long forgotten. "I haven't been around someone close to my own age in forever! Amelia Pond, the girl who's been torn out of her fairytale, and landed in my nightmare...I do believe you and I are going to be the best of friends!" she smiled, plump lips pulling wide over her straight white teeth. Amy had a feeling that the smile Mels was giving her would have made the Cheshire cat proud...

* * *

 _ **So, this is an all human Doctor Who AU, very Amy and River Centric...**_

 _ **I'm going to be squishing a number of Doctor Who villains together into 1 big bad organization, including ones who never actually met Amy or River, (*cough* Mrs Gillyflower *cough*) but this is my fic and... *does bad Loki impression* "I DO WHAT I WANT!"**_

 _ **since the villains main goal can no longer be to destroy an all powerful time travelling alien called The Doctor, I'm going to have to figure out exactly what The Silence is training River for, other than basic world domination. (I'm open to suggestions, since I have the basic idea planned out but no specifics yet)**_

 _ **The Doctor isn't going to appear till the very end od this story, but I'm planning to make a sequel that revolves around the Doctor more (I'm also considering making him have Multiple Personality Disorder, since he'll just be a regular human like everyone else, but I just can't imagine making him too normal...what do you think?)**_

 _ **as you can see, I've changed Amy and Rivers relationship rather drastically, but they never really had a normal Mother/Daughter bond anyway, so in this fic they'll be more like adoptive sisters.**_

 ** _I hope River, (or Mels, as she's currently being called) is ok, I'm trying to make it obvious that she's unstable. I mean, she is psychopath after all, and besides Rivers always seemed to have pretty major mood swings, enjoyed being a disrespectful delinquent (even as Mels the kid) and been far too blasé about violence due to her upbringing. obviously she also doesn't have to greatest social skills at the moment, but that will happen when you've been locked in a lab for 10 years. anyway, i hope it worked, you can tell she's brilliant, and she's not off-putting or anything..._**

 ** _Hope Amy's ok as well, I know she's not very fiesty right now, but she's still just a kid, and pretty shell-shocked at the moment._**

 ** _Sorry about the swearing, I don't normally use cuss words in my fics, but I wanted to show how River has had to grow up too fast..._**

 ** _I hope to update soon, and have a much shorter Authors note/longer chapter!_**

 ** _I don't own Doctor Who or any of its characters, and please review!_**


	2. The Vengeful Melody

Amy opened her eyes with a sigh and glanced over Mels uneasily. Two minutes after Mels' cheerful prophecy of friendship, the odd girl had stopped talking and started totally ignoring her.

Though she was confused by Mels' sudden disinterest in her, Amy was actually quite relieved to have some time to herself, and she felt much better now that she'd had a chance to think things over and calm down.

She had more or less come to terms with her current situation, and after going over their previous conversation in her head, she still didn't really understand half of what the other girl had said, but she now had a million questions for Mels, who was currently doing what looked like push-ups on her side of the bars. She cringed at how weepy and pathetic she must have sounded earlier, and quite frankly wasn't surprised Mels had stopped talking to her. Hopefully they could actually get something figured out now that she was feeling more like herself again.

Amy carefully stood up, wincing in pain as the room spun around her. She still didn't really know where she was, why she was here, or why the hell Mels had been doing push-ups for the last half hour, but she was determined to find out. Besides, she was starving, and Mels' promise of lunch and 'Ada' hadn't come true yet.

Slowly making her way over to the bars, Amy observed Mels for a few moments before awkwardly clearing her throat. "Uh, Mels?" Mels ignored her. "Mels?" Amy took a deep breath. "MELS!"

Mels finally glanced over at her and with one swift, smooth movement, pushed off the floor and onto her feet. Making her way over to the exasperated Amy, she leaned casually against the bars.

"So you're real then." she grinned, looking pleasantly surprised. "Cool."

"...I'm sorry, what?!" said Amy. So far this conversation wasn't going any better than the last one.

"See, Ada said she heard her mom and Kovarion talking about how they thought I was too isolated and if they didn't do something soon, I might go crazy -well, crazier- from loneliness and/or be unable to interact with people properly when I'm older, which would make me a really lame infiltrator and assassin. So when you got dumped in here, I figured there were two options. Either they decided to stick you in here with me to sharpen my social skills, or I'd totally lost it and was hallucinating."

"Why would you be hallucinating?!" Amy demanded, slightly miffed to be mistaken for imaginary.

"Well, I am a psychopath." Mels stated calmly, oblivious to Amy's sudden discomfort as she took a step back from the bars. What kind of a messed up kid could say something like that without batting an eyelash? "Plus I had a combat training session this morning, and I'm pretty sure my stupid Dalek combat instructor gave me a concussion. Sooo, y'know, it wasn't as unlikely as you'd think."

"...I don't know how to respond to that.." Amy stared at Mels, her nose scrunched up in confusion. "But I'm not made up!"

"Yeah, I can see that _now_ ," Mels rolled her eyes. "Thats why I was ignoring you. I figured if I pretended you weren't there, then you'd either disappear, which would mean you didn't really exist in the first place, or you'd get fed up and make me talk to you which would mean you were real." her expression clearly said she thought that should have been obvious to Amy.

"Then why did you talk to me when I first woke up?" She demanded, wishing Mels would just give Amy her full attention and stop doing the splits.

"I wasn't gonna, but then you started freaking out and screaming your head off, and I figured I wouldn't be able to ignore you till I'd calmed you down some.." Mels shrugged, standing back up and doing some jumping jacks.

Amy snorted, remembering Mels' unsympathetic looks, rude words, unhelpful answers, and angry ranting. "Yeah, great job being a kind and understanding ally against our captors." She muttered sarcastically. "I wish I had your people skills."

Mels scowled. "Hey! Cut me some slack here! You're the first person I've talked to who isn't Ada or an evil messed up bigot!"

"Well here's a tip," Amy snapped. "For future reference, when you're talking to someone, its weird to randomly start working out!"

Mels stopped doing cartwheels and wheeled around to face Amy with a sneer. "For your information, I have to be in tip top shape at all times, which is a bit difficult when I'm stuck in a cell half the time. If I'm not in peak physical condition, then I get punished. Besides, one of these days I'll get another chance to escape, and I have to be ready for it. One mistake and I'll be screwed."

"Escape?!" asked Amy, forgetting her earlier irritation as she gazed at Mels hopefully.

Mels nodded, her eyes gleaming. "Yeah, see, they created me to be smarter, stronger, faster andjust plain _better_ than anyone else. Which includes _them_. So one day they're gonna slip up, and when they do..." she smirked darkly and cracked her knuckles theatrically. " I'll be waiting."

"Huh," Amy snorted, her hope deflating like a balloon. "Sounds like wishful thinking to me. I mean, you don't even have a _plan_." She winced as soon as the words left her mouth, afraid that Mels would get angry again, but to her surprise, the other girl just shook her head and laughed.

"Oh Amy, you have no idea what I'm capable of. See these bars?" she rapped on them with her knuckles. "These are here because of me."

"...What do you mean?" Amy asked cautiously.

"This used be all one room. _My_ room. No bars _whatsoever_. But every time the guards came to drag me to another training session, or a 'meeting' with Dr Gillyflower, the second they opened the door, I'd try to make a break for it before they could snap the Electro-cuffs on."

"I'm sorry," Amy interrupted her, looking sick. "Did you just say _'Electro-cuffs'?!"_

"Yeah," Mels grimaced, rubbing her wrists subconsciously. "They're about as pleasant as they sound. Once those babies are on, if I make one wrong move they zap me with _way_ more volts than is healthy. Its like I've got tazers in my handcuffs, and once its activated, I'm not running away anywhere, I can barely _stand_. I can't imagine what it would do to a normal human."

Amy looked at Mels in shock. What the heck did she mean, _'normal human'_? Weren't all humans normal? And if not, what did that make Mels?

"Anyway," Mels cleared her throat awkwardly, seeming to realize she'd freaked Amy out a little.

"That's why I have to make a move before they get the cuffs on. I actually got out into the hallway once. I almost made it past the lab before they caught up to me. But I guess that kinda spooked them, made 'em realize they were underestimating me, cause they kept me drugged up for a week, and when I came to, these stupid things were here." She ran her hands over the bars absentmindedly.

"But, I don't get it." said Amy. "What do the bars do? Whats the point?"

"The point is, they can take their sweet time coming in here and locking the door, and I can't get at them until they come over here and unlock the bars. Which means that even if I do overpower them, I'll still be stuck in this room with a couple of dead or unconscious bodies at my feet."

"But you're still by the door then, right?" said Amy, trying not to freak out at the thought of Mels fighting what she assumed would be full grown men and winning. "Can't you just wait for someone else to open it and then get out?"

"Nope." Mels shook her head, popping the P loudly. "That's what I thought as well. A couple weeks after the damn bars showed up and they were a little less on edge I tried to escape again. It turns out that after the last incident, it became protocol that if my guards were taking longer than normal to get me, at least thirty other Silents would surround the door, armed with Tazers, tranquillizer darts and guns." She winced at the memory. " I barely even made it out the door." She smiled grimly "And of course I was punished severely for being insubordinate. So at the moment my plan is to do what they say, get my strength up, and get their guard down. Make them think I've given up and when the moment is right..." she made a fist and smirked. "I'll _crush_ them!" she declared gleefully.

"...Whats a Silent?" Amy asked curiously, not knowing what else to say to Mels painful sounding memories and unsettling thirst for revenge.

"Oh, them." Mels replied, not seeming to find this an odd response to her previous explanations. "That's just my little nickname for Kovarion's minions. (They're probably the ones who kidnapped you. They do most of the grunt work.) They don't really have names, so I named them. Its funny, cause the organization's called The Silence, and also cause they have no tongues." Mels laughed.

 _"WHAT?_!" Amy cried, curling her lip in disgust. "What do you mean, they have no tongues!"

"I mean they cut their tongues out." Mels said, looking unperturbed. "Its part of their initiation. They get injected with 'The Crimson Judgement' or whatever Dr. Gillyflower is calling it now, and if they survive then they cut out their tongue and shave their head. Its to prove their loyalty or something stupid like that. The tongue means they'll always be silent, and carry out the Silence's bidding. And the hair means they're giving up their individuality and names for the good of the Silence."

Amy stared at Mels in disbelief. "Thats insane! and how do you even know all this?! I thought you were locked up in here most of the time."

"I'm very observant." Mels smirked. "Besides, Ada-" she broke off mid-sentence and cocked her head to the side, listening intently. "Well speak of the devil!" she exclaimed, smiling broadly. "Sounds like she's finally here!"

* * *

 ** _Hey, so here's the next chapter! Sorry if the ending is a little abrupt, I wasn't sure how to end it._** ** _So what do you think of the beginning of my backstory on The Silence and who they are?_**

 ** _I figured Mels doesn't really respect authority, so she's unlikely to use the Madame in Madame Kovarion's name._** ** _Also, I know they're not really called 'Silents' but I needed something to call them other than 'pale creepy guys'_**

 ** _(Btw, I made a minor edit in the last chapter and changed Mels' approximate age and hair colour)_**

 ** _Oh yeah, and if anyone's interested, I recently wrote a bunch of random Doctor Who Limericks and posted them. I had a lot of fun writing them, and it would make my day if someone went to check it out! Its called 'There Once Was An Old Man From Gallifrey'_**

* * *

 _ **Adelaide Noble:**_  
 _ **I'm glad you like it! I couldn't see just making them live normal human lives, the adventures are a part of the characters! and don't worry, I'm not really focusing on romance at the moment.**_  
 _ **I'm glad you liked Melody, but how did she seem American? Was it her attitude, or her slang or what? Just curious, cause I'm Canadian, so I guess I don't really know the proper British terms and and way of talking. Watching Sherlock and Doctor Who can only do so much for a girl, but I'm trying my best. I tried to tone her down a little in this chapter, did it work?**_  
 _ **Hopefully Amy seems a little more like herself, now that she's calmed down a little...I'm trying to go for the more or less unruffled calmness and acceptance of the situation she displays when The Doctor crashes into her yard in the show, but sometimes she still freaks out a little, cause if you ask me, this situation is much scarier than an uncoordinated crazy guy who doesn't like your food and was sent by Santa.**_

* * *

 ** _Anyway guys, please review and tell me what you think!_**


End file.
